Begin paup; set autoclose increase=auto; log start file=Homogeneity.tests.log append; charset 12s = 1-433; charset 16s = 434-1037; [ charpartition all = 12s:12s, 16s:16s, dloop:dloop, s7:s7; [!ILD between all] hompart partition=all nreps=100 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq rstatus=no hold=1 swap=tbr multrees=yes; charpartition mit = 12s:12s, 16s:16s, dloop:dloop; exclude s7; [!ILD between mit] hompart partition=mit nreps=100 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq rstatus=no hold=1 swap=tbr multrees=yes; include all; [!ILD between 12S 16S] charpartition 1216S = 12s:12s, 16s:16s; exclude s7 dloop; hompart partition=1216S nreps=100 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq rstatus=no hold=1 swap=tbr multrees=yes timelimit=60; include all; [!ILD between 12S dloop] charpartition 12Sdloop = 12s:12s, dloop:dloop; exclude s7 16S; hompart partition=12Sdloop nreps=100 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq rstatus=no hold=1 swap=tbr multrees=yes; include all; [!ILD between 16S dloop] charpartition 16Sdloop = 16s:16s, dloop:dloop; exclude s7 12S; hompart partition=16Sdloop nreps=100 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq rstatus=no hold=1 swap=tbr multrees=yes timelimit=90; ] charpartition all = 12s:12s, 16s:16s, dloop:dloop, s7:s7; [!ILD between all] hompart partition=all nreps=100 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq rstatus=no hold=1 swap=tbr multrees=yes timelimit=60; charpartition mit = 12s:12s, 16s:16s, dloop:dloop; exclude s7; [!ILD between mit] hompart partition=mit nreps=100 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq rstatus=no hold=1 swap=tbr multrees=yes timelimit=60; log stop; end;